SMTL ID : 7q1h.1

Variant D312N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the substrate OMP at 1.31 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

homo-dimer

Ligands

2 x OMP: OROTIDINE-5'-MONOPHOSPHATE(Non-covalent)

OMP.1: 22 residues within 4Å: Chain A: S.35, K.59, H.61, N.90, K.92, N.119, I.146, M.149, S.150, I.179, P.195, G.196, Q.208, Y.210, I.226, V.227, G.228, R.229, G.230 Chain B: D.95, I.96, T.99 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.179, A:P.195 Hydrogen bonds: A:S.35, A:K.59, A:H.61, A:N.90, A:S.150, A:S.150, A:Q.208, A:Y.210, A:Y.210, A:Y.210, A:G.228, A:R.229, B:T.99 Water bridges: A:K.92, A:G.196, A:R.229, B:I.96, B:N.98 Salt bridges: A:K.59, A:K.92, A:R.229 OMP.4: 22 residues within 4Å: Chain A: D.95, I.96, T.99 Chain B: S.35, K.59, H.61, N.90, K.92, N.119, I.146, M.149, S.150, I.179, P.195, G.196, Q.208, Y.210, I.226, V.227, G.228, R.229, G.230 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.179, B:P.195 Hydrogen bonds: B:S.35, B:K.59, B:H.61, B:N.90, B:S.150, B:S.150, B:Q.208, B:Y.210, B:Y.210, B:Y.210, B:G.228, B:R.229, A:T.99 Water bridges: B:K.92, B:G.196, B:R.229, A:I.96, A:N.98 Salt bridges: B:K.59, B:K.92, B:R.229

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: V.38, S.39 Chain B: K.102 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.39, A:S.39 Water bridges: A:L.40, B:K.102, B:K.102, B:K.102 SO4.5: 3 residues within 4Å: Chain A: K.102 Chain B: V.38, S.39 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.39, B:S.39 Water bridges: B:L.40, B:E.43, A:K.102, A:K.102, A:K.102

2 x PRO: PROLINE(Non-covalent)

PRO.3: 6 residues within 4Å: Chain A: Q.198, E.200, A.201, G.202, G.203, Y.210 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:Y.210 Hydrogen bonds: A:A.201, A:G.203 PRO.6: 6 residues within 4Å: Chain B: Q.198, E.200, A.201, G.202, G.203, Y.210 3 PLIP interactions: 3 interactions with chain B, Hydrophobic interactions: B:Y.210 Hydrogen bonds: B:A.201, B:G.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rindfleisch, S. et al., Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis. Nat Catal (2022)

Release Date

2022-05-04

Peptides

Uridine 5'-monophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Uridine 5'-monophosphate synthase